Background: Despite considerable knowledge about musculoskeletal disorders (MSD) and physical, psychosocial and individual risk factors there is limited knowledge about physical activity as a factor in preventing MSD. In addition, studies of physical activity are often limited to either leisure activity or physical activity at work. Studies among military personnel on the association between physical activity at work and at leisure and MSD are lacking. This study was conducted to find the prevalence of MSD among personnel in the Royal Norwegian Navy and to assess the association between physical activity at work and at leisure and MSD. Methods: A questionnaire about musculoskeletal disorders, physical activity and background data (employment status, age, gender, body mass index, smoking, education and physical stressors) was completed by 2265 workers (58%) 18 to 70 years old in the Royal Norwegian Navy. Multiple logistic regression with 95% confidence intervals was used to assess the relationship between physical activity and musculoskeletal disorders. Results: A total of 32% of the workers reported musculoskeletal disorders often or very often in one or more parts of the body in the past year. The most common musculoskeletal disorders were in the lower back (15% often or very often), shoulders (12% often or very often) and neck (11% often or very often). After adjustment for confounders, physical activity was inversely associated with musculoskeletal disorders for all body sites except elbows, knees and feet. Conclusion: The one-year prevalence of musculoskeletal disorders among workers in the Royal Norwegian Navy was rather low. A physically active lifestyle both at work and at leisure was associated with fewer musculoskeletal disorders among personnel in the Royal Norwegian Navy. Prospective studies are necessary to confirm the cause and effect in this association